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Sample GSM4820562 Query DataSets for GSM4820562
Status Public on Dec 07, 2020
Title blood_17
Sample type genomic
 
Source name blood from coccygeal vein in the tail
Organism Bos taurus
Characteristics digital dermatitis binary phenotype: case
digital dermatitis quantitative phenotype: 0.4
farm: A
Sex: female
tissue: whole blood
Extracted molecule genomic DNA
Extraction protocol Whole blood sampled from the coccygueal vein of the tail were centrifuged, and the resulting buffy coat layer was stored at 4C until DNA extraction. Genomic DNA was extracted from buffy coat using the QIAGEN QIAamp DNA Blood Mini Kit according to the manufacturer's instructions.
Label C-Bio, G-Bio, A-DNP, T-DNP
Label protocol According to the Infinium HD Super Assay documentation (https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/infinium_assays/infinium-hd-super-assay/infinium-hd-super-assay-reference-guide-11322427-03.pdf), labels were added during allele-specific base extension.
 
Hybridization protocol Hybridization was performed according to the Infinium HD Super Assay documentation using the automated protocol.
Scan protocol Scanning was performed according to the Infinium HD Super Assay documentation using the automated protocol.
Description Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Data processing The Illumina GenomeStudio Genotyping Module was used to determine genotypes from the intensity data files (IDAT files) outputted from scanning the BeadChip.
The Illumina GenomeStudio Genotyping Module called genotypes and generated SNP statistics.
 
Submission date Oct 07, 2020
Last update date Oct 20, 2021
Contact name Anita Oberbauer
Organization name University of California, Davis
Department Animal Science Department
Lab Oberbauer Lab
Street address One Shields Ave.
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
 
Platform ID GPL21267
Series (1)
GSE159157 Genome-wide association studies reveal susceptibility loci for digital dermatitis in Holstein cattle
Relations
Alternative to GSM5642192

Supplementary file Size Download File type/resource
GSM4820562_201879890056_R08C01_Grn.idat.gz 5.2 Mb (ftp)(http) IDAT
GSM4820562_201879890056_R08C01_Red.idat.gz 5.2 Mb (ftp)(http) IDAT
Processed data are available on Series record

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